Eight large-scale RNAi libraries designed for the Drosophila genome (Ambion, HD2, HFA/DRSC v1.0, DRSC v2.0, OpenBiosystems v1/v2, MRC, NIGFLY and VDRC) were re-annotated using the FlyBase annotations of release 5.24.
NEXT-RNAi HTML ouputs for the library evaluations are available here:
Pairwise comparisons of libraries
We used NEXT-RNAi results to identify the number of genes that could be targeted with independent designs through pairwise combinations of all Drosophila RNAi libraries. A summary report for all pairwise combinations is contained in libComparison_report.txt (44KB).
A detailed analysis for each combination of two libraries mapping reagents available for a certain target gene in one library to the reagents for this gene available in the other library (including information whether these reagents are 'completely', 'partially' or 'not' independent ) is available for download (libComparison.tar.gz (15MB).
Input files and settings used
Input FASTA files
Ambion, DRSC v2.0 and HD2 libraries were evaluated using long dsRNA sequences as input; HFA/DRSC v1.0, OpenBiosystems v1/v2, MRC and VDRC libraries were evaluated using both, primer and long dsRNA sequences as input and the NIGFLY library was evaluated starting from primers.
- Ambion long dsRNAs: ambion_amplicon.fa (3.3MB)
- HD2 long dsRNAs: HD2Designs_Batch123.fasta (7.2MB)
- HFA/DRSC v1.0 primer and long dsRNAs: HFA_primer.fasta (1.4MB), HFA_dsRNA.fasta (8.6MB)
- DRSC v2.0 long dsRNAs: v2_seqs_MOD.fa (11MB)
- OpenBiosystems v1/v2 primer and long dsRNAs: ob_v01_v02_primer.fasta (960KB), ob_v01_v02_dsRNA.fasta (7.2MB)
- MRC primer and long dsRNAs: mrc_primer.fa (1.1MB), mrc_amplicon.fa (7.4MB)
- NIGFLY primer: nigfly_primer.fa (740KB)
- VDRC primer and long dsRNAs: vdrc_primer.fa (1.1MB), vdrc_amplicon.fa
Targetgroup file (tab-delimited)
FBtr-FBgn-CG-Txn-Name-r5.24.tab (1.4MB) defining which FlyBase transcripts belong to the same gene (headers Target and TargetGroup) (TARGETGROUPS option)
Bowtie database/index for off-target evaluation
Bowtie database/index containing annotated FlyBase (release 5.24) transcripts for specificity calculations (-d input):
Bowtie database/index for mapping of reagents
The Bowtie database/index (GENOMEBOWTIE option) for mapping of reagents to the Drosophila genome:
Bowtie indexes for genomes are also available through the Bowtie webpage.
Feature file with UTR locations
Tab-delimited feature file containing FlyBase mappings of UTRs to chromosomes that is used to calculate the 'UTR-content' (FEATURE option) of designed reagents: dmel-all-UTRs-r5.24.zip (65MB)
FASTA file for homology evaluation
Transcriptome FASTA file to evaluate the homology of the designs using Blast (HOMOLOGY option):
FASTA file containing miRNAs (miRBase)
Start of program
Descriptions for start parameters used are available here.
The same options file was used for all evaluation runs.
Descriptions for all options used are available here.